Abstract 5021: Accurate quantification of infiltrating B cell composition and clone diversity in tumor samples
Authors: Fabio Navarro, Eric Levy, Pamela Milani, Qiang Li, Shruti Bhide, Upasana Dutta, Charles W. Abbott, Jose Jacob, Rena McClory, John West, John Lyle, Sean Boyle, Richard O. Chen
Journal: Cancer Research (2022)

Abstract Tumors harbor a complex ecosystem of malignant, immune, and stromal cells. While malignant cells dictate much of the tumor biology, there is evidence that the tumor microenvironment (TME) also plays a major role in disease etiology. Given the complexity and abundance of the TME cellular composition, investigating the role of immune cell types will yield novel biomarkers for tumor progression and response to therapies. The role of B cells as a prognostic biomarker remains elusive. For instance, infiltrating B cells in CRC have both positive and negative prognostic value. Thus, a scalable approach to quantify B cells and the B-cell receptor (BCR) repertoire could yield novel insights into the role of B cells in tumor biology. To address this, we have developed immune cell quantification (InfiltrateID࣪) and immune receptor repertoire profiling (RepertoireID࣪) methods as part of the ImmunoID NeXT Platform®, an augmented, immuno-oncology-optimized exome/transcriptome platform. We estimate B cell abundance and BCR repertoire by profiling FFPE and PBMC samples using ImmunoID NeXT࣪. In expanding upon InfiltrateID to further estimate B cell abundance, here we regress the bulk RNA-seq readout from a reference signature from purified immune cell types. We also generate orthogonal quantifications of B cell abundance by profiling samples with cytometry by time of flight, single-cell RNA-seq, flow cytometry, and immunohistochemistry (IHC). We compare BCR results from ImmunoID NeXT to a standalone sequencing approach to evaluate the concordance of top clones. We then utilize BCR profiling from ImmunoID NeXT to analyze clonality and isotype composition in tumor samples. We first use InfiltrateID to estimate absolute B cell fractions in over 50 samples. Overall, we observe a high correlation between InfiltrateID results and orthogonal data sets in both PBMC and tumor FFPE samples (R2=0.90). When comparing BCR results from RepertoireID to a standalone BCR sequencing method that profiles IgM and IgG, we identify 475 and 387 of the top 500 clones in IgG and IgM, respectively, with highly concordant abundances across all clones (R2&amp;gt;0.72 and R2&amp;gt;0.82 in IgM and IgG, respectively). Next, we use InfiltrateID to estimate absolute B cell fractions in over 650 samples from 14 tumor types. On average, samples display B cell fractions in agreement with the literature and IHC quantifications, with higher B cell fractions in lung, breast, and cervical tumors. We also observe a range of BCR clonality values across tumor types. Finally, we observe differences in B cell composition and repertoire diversity in tumor samples from patients who underwent checkpoint blockade therapy. We show that InfiltrateID and RepertoireID accurately capture the composition and clone diversity of infiltrating B cells in tumor samples. Citation Format: Fabio Navarro, Eric Levy, Pamela Milani, Qiang Li, Shruti Bhide, Upasana Dutta, Charles W. Abbott, Jose Jacob, Rena McClory, John West, John Lyle, Sean Boyle, Richard O. Chen. Accurate quantification of infiltrating B cell composition and clone diversity in tumor samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5021.